A plugin for exporting RDF from OMERO

• OMERO 5.6.0 or newer
• Python 3.10, 3.11, or 3.12 (only versions with zeroc-ice binary wheels are supported; newer versions will be added when wheels are available)

This section assumes that an OMERO.py is already installed and zeroc-ice is configured.

Install the command-line tool using pip:

$ pip install -U omero-rdf

Using uv (recommended):

1. Fork/clone the repository (e.g. gh repo fork https://github.com/German-BioImaging/omero-rdf).

2. Create a virtualenv and activate it:

   uv venv .venv
   source .venv/bin/activate
   

   (or prefix commands with uv run instead of activating).

3. Install in editable mode with test dependencies:

   ::

   uv pip install -r zeroc-ice-requirements.txt uv pip install -e ".[tests,dev]"

4. Run the test suite:

   pytest test/unit
   pytest test/integration/test_idr
   

5. Lint and format:

   ruff check
   ruff format --check
   ruff format
   

To run pre-commit hooks:

uv tool install pre-commit
pre-commit run --all-files

Assuming you have the uv environment active (source .venv/bin/activate), use the public IDR server to confirm the CLI works (public credentials):

1. Log in once to create a session:

   omero login -s idr.openmicroscopy.org -u [PUBLIC USER] -w [PUBLIC PASSWORD]
   

2. Export RDF for a project on IDR (2902) and inspect the first triples:

   omero rdf -F=turtle Project:2902 -S=flat | head  -n 10
   

Mocking GitHub Actions checks

1. If you have gh installed, you can run the checks locally:

   gh act push
   

This repository uses versioneer to manage version numbers. A tag prefixed with v will be detected by the library and used as the current version at runtime.

Remember to git push all commits and tags.

Funded by the Delta Tissue Program of Wellcome Leap.

This project, similar to many Open Microscopy Environment (OME) projects, is licensed under the terms of the GNU General Public License (GPL) v2 or later.

2022-2026, German BioImaging